After Brook questions the origin of the Mini Merry name, Usopp and Chopper Tony Tony recall the adventures of the Straw Hat Crew's beloved ship, friend, and crew member—the Going Merry. Ussop abandons the crew for a fight over the Going Merry while Robin Nico leaves with the government's top assassin group, CP9. In order to bring the crew back together, Monkey D. Luffy and the remaining Straw Hats follow Robin to rescue her from the claws of the World Government.

The tests have come, and Keitaro can only hope to succeed. However, in the final stretch, he fails miserably and daydreams through the test. Assuming that he has failed, he runs away, so the rest of the cast hunts him down on a remote desert island to bring him back. The Toudai entrance exams have finally come (again) for Keitaro. With all his confidence Keitaro sits for the paper, but ends up falling asleep and dreaming about Narusegawa. Waking up with barely any time to complete the paper, Keitaro thinks he will fail the paper and tries to escape from Hinata Lodge and forget all the memories with it. By a stroke of luck he meets Seta, but ends up in a faraway island with the whole cast trying to look for him. (Source: ANN)

After conquering the galaxy, mankind has reached its apex and is now on a steady decline. The resources of the universe are diminishing, and around 500 billion humans begin to return home to Earth. Thus begins a war between the various factions of humans for control of the planet. Eventually, an authoritarian government known as the Gaia Sanction prevents the re-population of Earth. Captain Herlock was one of the Elite Wing who was tasked by the Gaia Sanction to defend the Earth. His fleet of ships was unstoppable under his command. However, the Gaia Sanction allows a diplomatic elite to immigrate to Earth, which angers Herlock. He goes rogue and fires upon the diplomats and the rest of his fleet. He decides to unleash dark matter on the planet to make it uninhabitable, but also becomes engulfed in it which immortalizes him. One hundred years have passed, and the legendary Captain Herlock is still at large, with only the Arcadia under his control. The Gaia Sanction continues with their plans for control over the Earth, while hiding its true state. But Captain Herlock is preparing for one final showdown with them, which will determine the fate of the world!

Akari Mizunashi continues her training to become a Prima Undine (a professional tour guide gondolier) along with her friends Aika and Alice in the peaceful city of Neo Venezia. Despite the fact that these three girls are from competing companies, they are constantly together, learning more about how to become better tour guides and more about the mysteries of Neo Venezia. As the group continues to meet interesting and unforgettable people through their daily routines, they will also come closer to the secrets that make the enigmatic and ever beautiful city of Neo Venezia so warm and alive. Welcome back to Neo Venezia: the city where miracles can be created by hand.